León Bernal, Kanwar Samiah, Aguilar Olga, Chacón Idania, Cháves Gisela, Spiro David J, Tamim Sana, Trovao Nidia S
Virology Lab-LSE, Veterinary Services National Laboratories (LANASEVE), Animal Health National Service (SENASA), Ministry of Livestock and Agriculture (MAG), Heredia, Costa Rica.
Department of Paediatrics and Child Health, The Aga Khan University, Stadium Road, Karachi, Pakistan.
bioRxiv. 2025 Aug 22:2025.08.22.671733. doi: 10.1101/2025.08.22.671733.
In August 1995, necropsies on post-weaning piglets from the CA-CART farm in the province of Cartago, Costa Rica, revealed respiratory lesions, pleuritis, peritonitis, and arthritis. Skin lesions were also observed, progressing to scabs. A subsequent outbreak in 1996 prompted antibiotic administration. Mortality analysis from 1990 to 1995 showed no significant seasonal patterns, but yearly variations were noted. Piglets born in Costa Rica from imported gilts had a higher average mortality rate (10.65%) than the 8.11% mortality rate for piglets born from non-imported gilts and sows or imported sows (p = 0.002).
In March 1996, serum samples were sent for potential PRRS virus (PRRSV) diagnosis, and 10 PRRSV-2 ORF5 sequences collected during a prospective study from 2019-2021 were obtained from various locations in the country. In this article, we seek to investigate the evolutionary and spatio-temporal dynamics of PRRSV-2 in Costa Rica in the context of international swine movements using the phylodynamic framework integrated with the BEAST package.
The phylodynamic modeling estimated at least two independent PRRSV-2 introductions into the country. The earliest introduction occurred around 1978 (95% highest posterior density interval: 1959.01-1997.54) and led to the viruses circulating in the farm 1CRC with an origin from Japan, possibly via US swine exports. A second cluster, 4CRC, subsequently emerged within Costa Rica from the earlier 1CRC lineage (1990.24; 95% HPD interval = 1976.15-2010.30). Another viral introduction from the US occurred around 1991 (95% highest posterior density interval: 1974.34-2011.35) and established the 3CRC cluster. Though the viral introduction was traced back to the US, the limited genomic surveillance of PRRSV leaves room for considering alternative origins.
Our findings provide a high-resolution model of how international swine trade drives the introduction and evolution of a major livestock pathogen, highlighting the critical need for integrating genomic surveillance into biosecurity protocols.
1995年8月，对哥斯达黎加卡塔戈省CA - CART农场断奶后仔猪进行的尸检显示有呼吸道病变、胸膜炎、腹膜炎和关节炎。还观察到皮肤病变，病变发展为结痂。1996年随后爆发的疫情促使使用抗生素。1990年至1995年的死亡率分析显示没有明显的季节性模式，但注意到年度变化。哥斯达黎加进口后备母猪所产仔猪的平均死亡率（10.65%）高于非进口后备母猪、母猪或进口母猪所产仔猪8.11%的死亡率（p = 0.002）。
1996年3月，采集血清样本进行潜在的猪繁殖与呼吸综合征病毒（PRRSV）诊断，并从前瞻性研究（2019 - 2021年）期间该国不同地点收集了10个PRRSV - 2开放阅读框5（ORF5）序列。在本文中，我们试图利用与BEAST软件包集成的系统发育动力学框架，在国际生猪流动的背景下研究哥斯达黎加PRRSV - 2的进化和时空动态。
系统发育动力学模型估计至少有两次独立的PRRSV - 2传入该国。最早的传入发生在1978年左右（95%最高后验密度区间：1959.01 - 1997.54），导致在1CRC农场中传播的病毒起源于日本，可能是通过美国的生猪出口。随后，第二个集群4CRC在哥斯达黎加境内从较早的1CRC谱系中出现（1990.24；95% HPD区间 = 1976.15 - 2010.30）。1991年左右发生了另一次来自美国的病毒传入（95%最高后验密度区间：1974.34 - 2011.35）并形成了3CRC集群。尽管病毒传入可追溯到美国，但PRRSV有限的基因组监测为考虑其他起源留出了空间。
我们的研究结果提供了一个高分辨率模型，展示了国际生猪贸易如何推动一种主要家畜病原体的传入和进化，突出了将基因组监测纳入生物安全协议的迫切需求
